Molecular Biotechnology最新文献

{"title":"Glycoprofile Comparison of the SARS-CoV-2 Spike Proteins Expressed in CHO and HEK Cell Lines.","authors":"Helen L Wright, Caroline Evans, Philip J Jackson, David C James, Kang Lan Tee, Tuck Seng Wong, Mark J Dickman, Jagroop Pandhal","doi":"10.1007/s12033-024-01288-2","DOIUrl":"https://doi.org/10.1007/s12033-024-01288-2","url":null,"abstract":"<p><p>Coronavirus SARS-CoV-2 spike protein remains a key focus of research due to a continued need for diagnostic and therapeutic tools to monitor and respond to new variants. Glycosylation of the spike protein is critical for the protein's functions in viral attachment and host cell entry. For scalable and cost-effective production of the spike protein, expression system-driven divergence in glycosylation patterns on recombinant spike proteins needs to be fully understood. This study assessed the N-glycosylation profiles of a full-length trimeric spike protein expressed in either Human Embryonic Kidney (HEK Expi293F) or Chinese Hamster Ovary (CHO-S) cells. Glycopeptide analysis was performed using a tandem mass spectrometry workflow and BioPharma <math> <msup><mrow><mtext>Finder</mtext></mrow> <mtext>TM</mtext></msup> </math> incorporating HEK and CHO glycan databases for protein characterisation. The results outline important differences in the variety and types of N-glycan generated by the two cell lines across the 22 known N-glycosylation sites of the spike protein. A notable increase in terminal sialylation, as well as the presence of the potentially immunogenic N-glycolylneuraminic acid at a functionally key N-glycosylation site, was observed in the CHO-S derived spike protein. With the potential for the relatively vast and more complex CHO glycan repertoire (182 glycans relative to 39 human glycans) to produce functional implications with CHO-S expressed spike protein, this study adds valuable knowledge to aid Quality by Design approaches and enable Multi Attribute Monitoring of specific N-glycosylation sites for proteoform analyses. This can further inform antigen development with future variants in order to devise updated diagnostic tests and therapeutic vaccine designs.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142350373","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"ZNF217 Mediates Transcriptional Activation of GRHL3 to Regulate SLC22A31 and Promote Malignant Progression in Thyroid Cancer.","authors":"Ying Xu, Chunxu Liu, Qingrui Meng","doi":"10.1007/s12033-024-01292-6","DOIUrl":"https://doi.org/10.1007/s12033-024-01292-6","url":null,"abstract":"<p><p>The incidence of thyroid cancer (THCA) has increased worldwide during the past 40 years. However, an understanding of the mechanisms and major transcription factors involved in THCA is insufficient to identify therapeutic targets against THCA. To reveal such mechanisms, we conducted bioinformatics analyses to assess the differential expression in human THCA sample and normal tissue sample, leading us to focus on the function of the ZNF217/GRHL3/ SLC22A31 axis in mediating biological activity in THCA. The genes of interest were interfered with lentiviral vectors, and transfection efficiency was verified using RT-qPCR. ZNF217, GRHL3, and SLC22A31 were abundantly expressed in THCA tissues or cells. Knockdown of GRHL3, ZNF217, or SLC22A31 all significantly curtailed the malignant biological behavior of THCA cells. ZNF217 promoted GRHL3 expression through transcriptional activation, thereby increasing the transcription of SLC22A31. Ectopic expression of GRHL3 or SLC22A31 abated the suppressing impact of ZNF217 or GRHL3 knockdown on the biological activity of THCA cells. Collectively, our results demonstrated that ZNF217 acted as an activator of GRHL3, thereby promoting the expression of SLC22A31 and the malignant activity of THCA cells.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142361788","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Inhibitory Effects of Anti-GPC3 Antibody on Wnt/β-Catenin Signaling Pathway as a Biological Therapy in Liver Cancer.","authors":"Qin Gan, Jia Shao, Tingli Sun","doi":"10.1007/s12033-024-01291-7","DOIUrl":"https://doi.org/10.1007/s12033-024-01291-7","url":null,"abstract":"&lt;p&gt;&lt;p&gt;To investigate the effects of anti-GPC3 antibody on the Wnt/catenin pathway in liver cancer biology, thus providing a new target for the biological treatment of the disease. A total of 12 BALB/C experimental nude mice were selected as experimental objects. The mice were all male, weighed 15-20 g and aged 4-5 weeks. First, mouse liver cancer models were constructed. Then, the HepG2 liver cancer cells in logarithmic growth period were inoculated into the caudal veins of mouse models. On the 3rd day after inoculation, the tumor formations of nude mice were observed. Second, the anti-GPC3 antibody was designed and constructed, and the activity of anti-GPC3 antibody was detected. The mouse models were divided into the experimental group (EG) and the control group (CG), with 6 mice in each group. In the EG, mice were injected with 3 mg/kg of anti-GPC3 antibody in the caudal veins once a day for three consecutive days, while in the CG mice were injected with the same amount of saline as the control. Mice in both groups received 3 injections in total. After the last administration, all mice were euthanized using the decapitation method following anesthesia with ethyl ether. The liver cancer cells of nude mice were extracted and cultured in DMEM medium. The effects of anti-GPC3 antibody on Wnt/β-catenin in liver cancer nude mice and the effects of anti-GPC3 antibody on epithelial-mesenchymal transition (EMT) in mouse liver cancer cells were observed. The bodyweight, liver weight and index of mice in the EG increased significantly (P &lt; 0.05). The serum alanine transaminase (ALT), aspartate transaminase (AST), alkaline phosphatase (ALP) levels of mice in the EG were reduced than those in the CG (P &lt; 0.05). Compared with the CG, the superoxide dismutase (SOD) concentration increased, while the malonaldehyde (MDA) concentration decreased in the liver tissues of mice in the EG (P &lt; 0.05). There was binding activity between GPC3 recombinant protein and the antibody; the affinity constant was K&lt;sub&gt;D&lt;/sub&gt; = 1.4 × 10&lt;sup&gt;-6&lt;/sup&gt; M, compared with the commercial anti-GPC3 antibody, the affinity constant was lower. The interference effects of siRNA on anti-GPC3 antibody were detected by Western Blot. After the injection of anti-GPC3 antibody, the expression of β-catenin siRNA in liver cancer cells decreased significantly. The optical microscope images of mouse liver cancer cells in groups were compared. Through down-regulating the Wnt/β-catenin by anti-GPC3 antibody, the morphology of epithelial cells was maintained, the cells were arranged orderly, the cubic structure was kept stable, and the occurrence of EMT was reduced. However, in the CG, the structure of mouse liver cancer cells was disordered, the obvious EMT occurred (P &lt; 0.05). Through down-regulating the expression of Wnt/β-catenin by anti-GPC3 antibody, the invasiveness, and metastasis of liver cancer cells could be effectively inhibited. Compared with the CG, the number of cells passing through t","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142350376","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Proteins with Anti-apoptotic Action in the Hemolymph of Caterpillars of the Megalopygidae Family Acts by Maintaining the Structure of the Cellular Cytoskeleton.","authors":"Nathalia Delazeri de Carvalho, Henrique Krambeck Rofatto, Karina de Senna Villar, Roberta Fiusa Magnelli, P I Silva Junior, Ronaldo Zucatelli Mendonça","doi":"10.1007/s12033-024-01271-x","DOIUrl":"https://doi.org/10.1007/s12033-024-01271-x","url":null,"abstract":"<p><p>Brazil has a very large biological variety, which is an almost inexhaustible source of substances of pharmacological and biotechnological interest. Several studies have demonstrated the presence of bioactive peptides in insect hemolymph and their potential use as therapeutic agents. However, few data are available regarding molecules extracted from insects with anti-apoptotic action. The objective of this work was to identify the presence of proteins from the hemolymph of caterpillars of the Megalopygidae family with pharmacological and biotechnological interest. This study provides preliminary and innovative information on a new substance that inhibits cellular apoptopsis and stabilizes the tested cells, impacting the cytoskeleton, maintaining cellular structure and its functions. To this, two species of Megalopygidae family were studied, Podalia sp. and Megalopyge albicolis. Cytotoxicity tests on Vero and Sf-9 cells revealed that the hemolymph of both caterpillars was cytotoxic only at concentrations greater than 5%v/v. In the anti-apoptotic activity assays, it was verified that the supplementation of cell cultures with only 1% of hemolymph v/v is sufficient to inhibit cell death by apoptosis induced by different inducers such as terbutyl, actinomycin D, hydrogen peroxide, or even by nutrient depletion. For this study, cells were stained with trypan blue, crystal violet, and fluorescent markers to cytoskeleton (actin and tubulin), mitochondria membrane electric potential (JC-1), and apoptosis marker (acridine orange and ethidium). The protein responsible for anti-apoptotic action was isolated through gel filtration chromatography, using an AKTA purifier high-resolution liquid chromatography system. The hemolymph was fractionated into 3 pools for Podalia sp. and 6 pools for M. abicolis. In the antiapoptotic tests, semi-purified hemolymph from both caterpillars showed anti-apoptotic effect in VERO and SF-9 cells, pre-treated with only 1% v/v of hemolymph and induced to death by different and apoptotic inductors. Was observed that the molecule with anti-apoptotic effect is present in pool 3 in both hemolymphs. This protector effect blocked and attenuated the disruption of the cytoskeleton (actin filaments), being that the protective effect also was observed on the integrity of the mitochondrial membrane of SF-9 cells pre-treated with both hemolymphs and treated with the apoptosis inducer Terbutil at concentrations of 25 to 100 µM. By acting on the mitochondrial pathway of death by apoptosis, and by maintaining the structure of the cytoskeleton and cellular functions, pathway that can cause disorders and diseases neurodegenerative, the substances present in the hemolymph of these and other caterpillars could be good candidates in studies for the treatment of neurodegenerative diseases such as Parkinson's disease and Alzheimer's.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142350374","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Recent Advances in Marine-Derived Nanoformulation for the Management of Glioblastoma.","authors":"Chanam Melody Devi, Kangkan Deka, Amit Kumar Das, Apurba Talukdar, Piyong Sola","doi":"10.1007/s12033-024-01287-3","DOIUrl":"https://doi.org/10.1007/s12033-024-01287-3","url":null,"abstract":"<p><p>Glioma is the most common and aggressive type of central nervous system tumor as categorized by the World Health Organization. Glioblastoma (GBA), in general, exhibits a grim prognosis and short life expectancy, rarely exceeding 14 months. The dismal prognosis is primarily attributed to the development of chemoresistance to temozolomide, the primary therapeutic agent for GBA treatment. Hence, it becomes imperative to develop novel drugs with antitumor efficacy rooted in distinct mechanisms compared to temozolomide. The vast marine environment contains a wealth of naturally occurring compounds from the sea (known as marine-derived natural products), which hold promise for future research in the quest for new anticancer drugs. Ongoing advancements in anticancer pharmaceuticals have led to an upswing in the isolation and validation of numerous pioneering breakthroughs and improvements in anticancer therapeutics. Nonetheless, the availability of FDA-approved marine-derived anticancer drugs remains limited, owing to various challenges and constraints. Among these challenges, drug delivery is a prominent hurdle. This review delves into an alternative approach for delivering marine-derived drugs using nanotechnological formulations and their mechanism of action for treating GBA.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142350375","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development and Validation of a Highly Sensitive RT-qLAMP Assay for Rapid Detection of SARS-CoV-2: Methodological Aspects.","authors":"Faezeh Mahmoudi, Davod Jafari, Seyedeh Mona Mousavi Esfahani, Arshad Hoseini, Mahmood Barati, Neda Saraygord-Afshari","doi":"10.1007/s12033-024-01275-7","DOIUrl":"https://doi.org/10.1007/s12033-024-01275-7","url":null,"abstract":"<p><p>Specific and reliable diagnostic methods are becoming increasingly essential to identify patients in light of the high transmission rate and the recent appearance of the new variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). For the specific detection of SARS-CoV-2, our quantitative reverse transcription loop-mediated isothermal amplification (RT-qLAMP) assay implementation demonstrates how flexible it can be with two readouts: visualized colorimetric and real-time fluorescence. Different factors were optimized to improve the reaction conditions, including temperature (60 °C), assay runtime (60 min), primers, MgSO₄ (6 mM), dNTPs (1 mM), LAMP Buffer (1.2 mM Tris-HCl), KCl (50 mM), pH (8), and phenol red (10 mM) concentrations. Regarding analytical sensitivity, the colorimetric RT-LAMP method detected samples with C_t values up to 29, while the RT-qLAMP assay identified up to C_t = 31. RT-qLAMP was evaluated on 40 clinical samples (25 positives and 15 negatives) for viral RNA detection. All negative samples were found negative through fluorescent reading in RT-qLAMP and quantitative reverse transcription PCR (RT-qPCR) assays. Twenty-three clinically positive samples demonstrated a positive RT-qLAMP reaction (up to C_t ≤ 31) with 92% clinical sensitivity, 100% clinical specificity, 100% positive predictive value (PPV), 88.24% negative predictive values (NPV), and 95% accuracy.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142308159","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Codon Optimization is Required to Express Fluorogenic Reporter Proteins in Lactococcus lactis.","authors":"América Selene Gaona-Mendoza, Julio Armando Massange-Sánchez, José Eleazar Barboza-Corona, María Jazmín Abraham-Juárez, Luz Edith Casados-Vázquez","doi":"10.1007/s12033-024-01285-5","DOIUrl":"https://doi.org/10.1007/s12033-024-01285-5","url":null,"abstract":"<p><p>Lactococcus lactis is a Gram-positive bacterium used to produce fermented foods and heterologous proteins. Its Nisin-controlled gene expression system stands out for its versatility and safety. However, the lower GC content in its genome may lead to some limitations in protein production. In this study, we explored the importance and effect of codon optimization on fluorescent reporter protein expression in L. lactis. Three non-optimized fluorescent reporter genes (gfp, rfp, and mcherry) were compared to the codon-optimized variant (mcherry-O). Parameters such as Codon Adaptation Index (CAI), Effective Number of Codons (Enc) and Guanine-Cytosine percentage (% GC) were determined to assess their influence on gene expression and protein synthesis. The production of non-optimized fluorescent proteins does not correlate with their gene expression levels, except for the codon-optimized mCherry-O protein, which was detected in the SDS-PAGE gel and the extracted lysate (visually detected). Expression of the mcherry gene was similar to the mcherry-O gene, but protein was only detected with the optimized gene. The gfp gene showed the highest expression levels, but the quantity of protein was undetectable by SDS-PAGE. The rfp gene was revealed to be an optimized gene but not tailored for L. lactis. These findings underscore the necessity of comprehensive codon optimization for foreign genes in L. lactis and reveal intriguing complexities between expression levels, RNA stability and protein synthesis.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142291543","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evaluation of Differentially Expressed Candidate Genes in Benzo[a]pyrene Degradation by Burkholderia vietnamiensis G4","authors":"Marcela Marmitt, Guilherme Pinto Cauduro, Renan César Sbruzzi, Victor Hugo Valiati","doi":"10.1007/s12033-024-01284-6","DOIUrl":"https://doi.org/10.1007/s12033-024-01284-6","url":null,"abstract":"<p>Bacteria-mediated bioremediation is widely employed for its environmental benefits. The genus <i>Burkholderia</i> can degrade persistent organic compounds, however, little is known about its mechanisms. To increase this knowledge, <i>Burkholderia vietnamiensis</i> G4 bacteria were exposed to benzo[a]pyrene, a recalcitrant compound, and the expression of twelve genes of interest was analyzed at 1, 12 and 24 h. In addition, benzo[a]pyrene degradation, evaluation of cell viability and fluorescence emission of assimilated benzo[a]pyrene was performed over 28 days. The up-regulated genes were <i>xre</i>, <i>paaE</i>, <i>livG</i> and <i>pckA</i> at the three times, <i>ACAD</i>, <i>atoB</i>, <i>bmoA</i> and <i>proV</i> at 1 h and <i>AstB</i> at 12 h. These genes are important for bacterial survival in stress situations, breakdown and metabolization of organic compounds, and nutrient transport and uptake. Furthermore, a 52% reduction of the pollutant was observed, there was no significant variation in the viability rate of the cells, and fluorescence indicated an accumulation of benzo[a]pyrene after 24 h. Our study demonstrates the bacteria adaptability and ability to modulate the expression of genes at different times and as needed. This increases our understanding of biodegradation processes and opens new possibilities for using this bacterial strain as a tool for the bioremediation of contaminated areas.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142253868","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptome Analysis of Differentially Expressed Genes and Molecular Pathways Involved in C2C12 Cells Myogenic Differentiation","authors":"Lingjian Tao, Weixing Huang, Zhiyan Li, Wei Wang, Xinhuan Lei, Jiangjie Chen, Xiaoting Song, Fangying Lu, Shaohua Fan, Liwei Zhang","doi":"10.1007/s12033-024-01259-7","DOIUrl":"https://doi.org/10.1007/s12033-024-01259-7","url":null,"abstract":"<p>Muscles are essential tissues responsible for movement, stability, and metabolism, playing a crucial role in human health and well-being. A comprehensive understanding of muscle differentiation processes is imperative for combating muscle degenerative diseases such as muscular dystrophy. In this study, C2C12 cells were induced to differentiate into myotubes in vitro. Phenotypic changes were observed utilizing Gimsa and immunofluorescent staining techniques. RNA sequencing was conducted at distinct time points (0, 2, 4, and 7 days) during the differentiation process. To elucidate the underlying molecular mechanisms, differential expression analysis, gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, and Gene Set Enrichment Analysis (GSEA) were performed. Soft clustering of time series gene expression was employed to establish the expression patterns of differentially expressed genes (DEGs) at various time points during myogenesis. Additionally, quantitative reverse transcription PCR was utilized to validate gene expression from RNA-seq data at the mRNA level. Throughout the myogenic differentiation of C2C12 cells, notable morphological changes were observed, with myoblasts forming multinucleated myotubes by day 4 and plump elongated structures by day 7. Gene expression analysis revealed a substantial increase in DEGs as differentiation progressed, with a significant rise in DEGs from day 0 to day 7. Enrichment analysis highlighted key biological processes and pathways involved, including signal transduction and immune system processes, as well as pathways like chemokine and calcium signaling. Noise-robust soft clustering identified distinct temporal gene expression patterns, categorizing genes into upregulated, downregulated, and biphasic response clusters. The MYH family exhibited diverse expression changes, with Myh3, Myh13, Myh6, Myh7, Myh2, Myh8, Myh14, Myh7b, Myh1, and Myh4 upregulated, Myh10, Myh9, and Myh12 downregulated. Key transcription factors displayed dynamic expression patterns, which was crucial for the regulation of myoblast differentiation. A comprehensive and dynamic transcriptomic analysis of the C2C12 myoblast differentiation process has significantly enhanced our understanding of the key genes and biological pathways involved in myogenesis.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142253866","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification and Validation of Oxidative Stress-Related Biomarkers for Bronchopulmonary Dysplasia","authors":"Zhenzhuang Zou, Yunrong Li, Jiaying Liu, Bo Huang","doi":"10.1007/s12033-024-01281-9","DOIUrl":"https://doi.org/10.1007/s12033-024-01281-9","url":null,"abstract":"<p>The objective of this study was to identify and characterize oxidative stress (OS)-related biomarkers in bronchopulmonary dysplasia (BPD) through a combination of bioinformatics analyses and wet experiments. The study utilized the Gene Expression Omnibus database to obtain the mRNA expression profile dataset GSE32472. Differential expression analysis and functional enrichment analysis were employed to investigate the role of OS-related genes in BPD. Gene Ontology Function Enrichment Analysis and Gene Set Enrichment Analysis were conducted to understand the mechanisms behind the signature. Protein–protein interaction analysis to identify hub genes in BPD, and predictions were made for microRNAs (miRNAs), transcription factors (TFs), and potential medications targeting these genes. CIBERSORT was utilized to investigate the correlation between hub genes and the infiltration of immune cells. Hub genes were ultimately determined and confirmed using expression analysis, correlation analysis, receiver operating characteristic (ROC) analysis, and quantitative real-time PCR (qRT-PCR). A novel OS-related gene signature (<i>ARG1</i>, <i>CSF3R</i>, <i>IL1R1</i>, <i>IL1R2</i>, <i>MMP</i>9, <i>RETN</i>, <i>S100A12</i>, and <i>SOCS3</i>) was constructed for the prediction of BPD. We identified 18 miRNAs, 14 TFs, and 30 potential medications targeting these genes. ROC analysis further validated that these genes could diagnose BPD with high specificity and sensitivity. The qRT-PCR revealed that <i>IL1R1</i> and <i>ARG1</i> were highly expressed in the lung tissue of the model group, while the expressions of <i>RETN</i>, <i>SOCS3</i>, <i>IL1R2</i>, and <i>MMP</i>9 were decreased. This study demonstrated that <i>ARG1</i>, <i>CSF3R</i>, <i>IL1R1</i>, <i>IL1R2</i>, <i>MMP9</i>, <i>RETN</i>, <i>S100A12</i>, and <i>SOCS3</i> may serve as potential diagnostic biomarkers in BPD. Furthermore, a significant association between <i>IL1R1</i> and the pathogenesis of BPD is observed.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142253865","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}